Rice transposable elements: A survey of 73,000 sequence-tagged-connectors

As part of an international effort to sequence the rice genome, the Clemson University Genomics Institute is developing a sequence-tagged-connector [S TC) framework. This framework includes the generation of deep-coverage BAC libraries from O. sativa ssp. japonica c.v. Nipponbare and the sequencing o f both ends of the genomic DNA insert of the BAC clones. Here, we report a survey of the transposable elements (TE] in 73,000 STCs. A total of 6848 ST Cs were found homologous to regions of known TE sequences [E<10(-5)) by FAS TX search of STCs against a set of 1358 TE protein sequences obtained from GenBank. Of these TE-containing STCs (TE-STCs], 88% [6027) are related to r etroelements and the remaining are transposase homologs. Nearly all DNA tra nsposons known previously in plants were present in the STCs, including mai ze Ac/Ds, En/Spm, Mutator, and mariner-like elements. In addition, 2746 STC s were found to contain regions homologous to known miniature inverted-repe at transposable elements (MITEs]. The distribution of these MITEs in region s near genes was confirmed by EST comparisons to MITE-containing STCs, and our results showed that the association of MITEs with known EST transcripts varies by MITE type. Unlike the biased distribution of retroelements in ma ize, we found no evidence for the presence of gene islands when we correlat ed TE-STCs with a physical map of the CUGI BAC library. These analyses of T Es in nearly 50 Mb of rice genomic DNA provide an interesting and informati ve preview of the rice genome.